There are four main categories that fish diseases can be divided into: Bacterial, Fungal, Parasitic, and Environmental. Some conditions can be caused by more than one of these (like secondary fungal infections at the site of a bacterial infection, or bacterial infections caused by poor water conditions) and identifying the cause of the issue is often important to helping to resolve it. 

Bacterial Infections:Bacterial infections are some of the most common and widespread conditions in aquariums. They may looks like a rough white coating, red patches or red sores, frayed or deteriorating fins, cloudy eyes or other similar visible symptoms depending on the exact bacteria. The edges of sores may be white and fuzzy, especially in the case of a secondary fungal infection also affecting the site. General bacterial infections are usually caused by a wound or injury, or poor water conditions like high Ammonia or low pH. They may be worse in fish already stressed by transport, bullying by tankmates or poor or improper water parameters. It is important to get rid of any causes of the infection or any conditions that may be making it worse. ALWAYS test the water quality to make sure the pH and temperature are appropriate and the Ammonia and Nitrite levels are zero or very minimal; fix any levels that are off before attempting to treat or medicate. If the water quality is good, a medication can be used if necessary. Some infections will clear up on their own once the conditions are improved but some mild medications or dietary supplements can help the healing. In severe cases or with some tankmates, a stronger medication might be needed and should be done in a separate quarantine system.

Fungal Infections: Fungal infections usually look like a cottony patch on a fish, particularly around the edges of a wound. Waste like leftover food can also grow a fungus, as can ornaments that are improperly cleaned. Using some air fresheners, cleaners or oils in the vicinity of the tank can also cause a white coating to grow on surfaces. It looks like tufts of cotton and can appear anywhere on the fish, particularly around an existing wound.Fungal infections are usually a secondary condition that appears because the fish is already weakened by another problem. Slow-moving fish like Bettas are vulnerable to a body fungus if the water is too cold for the fish to remain active or if the fish's metabolism is slowed. Wounds may have a secondary fungal infection around the edges, especially if the water is dirty. Waste or decorations may grow a fungal coating if the water flow is too low to move the waste so it can be removed by the filtration. Improve the water flow, temperature, water conditions or other parameters that may be allowing the fungus to grow. Medication can be used in some cases but most mild fungal infections will clear up on their own once the cause is addressed. 

Parasites: Parasites in general are one of the most common aquarium maladies next to unsuitable water conditions. Parasites by definition are any organism that requires a host organism to live, often to the detriment of that host and may lead to the death of the host. The size of parasites varies greatly from tiny organisms like those responsible for Ich and Marine Velvet, to larger crustaceans and worms like flukes, anchor worms or fish lice. These parasites can also be external (living on the outside of the body of the fish) or internal (living inside the fish, often in organs like the digestive system). Common signs of parasites are rapid breathing, weight loss, white feces, sores or a flicking or scratching behavior against rocks and surfaces. Different parasites require different treatments and treatment methods and so should be carefully diagnosed before medicating or treatments.

Environmental Stress/Biological Conditions: Environmental stress can result from improper water conditions (temperature, pH, salinity, etc.), unsuitable decor (too much or too little vegetation or decorations, too intense or dim lighting, etc.) or exterior conditions like activity in the room around the tank or vibrations caused by an unstable surface or tapping on the tank. Some biological conditions like poor nutrition, improper diet or poor breeding can cause problems as well. Some of these stresses can be easily fixed while others can be more difficult. Poor health or unusual behavior (including jumping from or trying to jump from the tank) can hint towards something wrong with the fish’s environment. Researching all choices for an aquarium and observing behavior regularly can help an aquarist to notice these problems.

Some more specific diseases and conditions that aquarists commonly encounter. 

B  : Bacterial 

F  : Fungal  

P  : Parasitic 

E  : Environmental/Biological

Ammonia Burn ( E ) : As the name suggests, this is a burn-like injury caused by highly acidic ammonia build-up. Ammonia can cause open wounds on a fish’s body or damage to sensitive structures like their gills. These excessive ammonia levels are commonly caused by poor filtration or overstocking with too many fish or fish too large for the tank. Treatment includes eliminating the cause of the high ammonia level, neutralizing or removing the ammonia, and treating the wounds if necessary to avoid infection. 

Aeromonas ( B ): Aeromonas infections are caused by several species of bacteria that are opportunistic and will affect organisms with weakened immune systems. It can affect fish, amphibians and even humans in some cases. Koi and other pond fish are vulnerable to Aeromonas infections during the early spring and summer when temperature fluctuations can leave them vulnerable and weakened. Aeromonas attack organs and will digest gelatin and hemoglobin cells. It often appears as deep open sores on the body of a fish as well as causing severe weight loss as it attacks the internal organs. Aeromonas bacteria is very resistant to most medications and can be very difficult to treat. Strong gram-negative bacterial medications both in the water and in food treatments can be used. Injections are also sometimes used by veterinarians and biologists to treat larger fish.

"Black Ich” or “Black Spot” ( P ):This disease is a parasite infection caused by flatworms. It mainly affects tangs and surgeonfish and appears as small dark spots on the body of the tang. The fish may also flick or scratch against surfaces or may be less active than normal. The flatworm lays eggs on the body of the fish and drops off within a few days, leaving the eggs to hatch on the fish a few days after that. Treatment for Black Ich can include freshwater baths or antiparasitic medications with active ingredients like formalin.

Brooklynella ( P ): This parasitic infection is also known as “Anemonefish Disease” or “Clownfish Disease” due to its most common victim. It is a protozoan that usually spreads very quickly and is almost always fatal and has no commercially-effective treatments. It can first be seen as a fine sheen on the affected fish – usually newly captured or transported fish – but soon evolves to signs of physical stress to the fish, difficulty breathing, and excessive slime coat production. As this slime coat sloughs off the fish, it can spread the protozoans throughout a system to prompt quarantine of an infected fish is absolutely important. All tank equipment should be cleaned and sterilized well as well to avoid spreading the disease. As I mentioned, there are no medications that are known to be very effective on these protozoans, but medications like those containing formalehyde, malachite green and and methylene blue used in a quarantine tank can help. Do not use freshwater dips with this infection.

Columnaris/"Mouth & Tail Rot" ( B ,  F ): With this bacterial infection, the "tips" of the fish - lips, mouth, and tail - are affected first. They develop a milky-white coating and appear to "rot away". It may be accompanied by a cottony-looking secondary fungal infection. In some fish - Rainbowfish especially - the gram-negative Columnaris bacteria responsible for this condition cause saddle-like patches starting at the back and dorsal fin and extending down the sides of the fish. Both of these forms may appear at the same time or you may only see one at a time. Poor water quality or sudden changes to their environment can leave fish vulnerable to this bacteria. It is important to improve any of these negative conditions before treating, and if medicating, be sure to use a medication for gram-negative bacteria. 

Dropsy ( B ,  E ): This is an internal condition that causes multi-organ failure, and is very difficult to treat. It is usually caused by an internal bacterial infection that causes the fish to retain fluids internally but can be brought on by other conditions or environmental stress. The fish often look like "pine-cones", with their scales sticking out, off of their body. They are often listless, won't eat, and sit at the bottom or in one area of the aquarium. Remove this fish as soon as you can and treat it in a quarantine tank! If the fish is eating, treat its food with an antibiotic. If not, treat the tank water with a strong antibiotic and hope for the best. If dropsy isn't caught in its early stages (lethargy, swollen abdomen, swimming in a bizarre manner) it is almost always fatal.

"Fin Rot" ( B ,  F  ,  E ): Fin rot can be more of a symptom than a disease in some cases (outside of the Columnaris/ "Mouth & Tail Rot" described above) and is essentially just what the name describes. The fins on the fish, most often first noticed in the caudal (tail) fin, will appear to be rotting away and may be red and ragged. The fins may also appear white as a secondary fungal infection sets in in some cases. This is usually caused by a bacterial infection and can be the result of bullying or fin-nipping tankmates or poor water conditions. The cause of the condition should be address (water quality improved or aggressive tankmate removed) and the fish can be treated with an antibiotic or antibacterial medication.

Head and Lateral Line Erosion (HLLE) (  E ,  P ): Head and Lateral Line Erosion (HLLE) is seen mostly in saltwater tangs and angelfish but other fish are also susceptible. Another similar condition, known as Hole-in-the-head, is very similar in appearance but mainly affects large cichlids and freshwater fish. With HLLE, the area around the head and eyes and the length of the lateral line down each side of the fish’s body becomes pitted and can appear to be rotting away. While not usually fatal in itself, HLLE can cause permanent scarring and is a symptom of a more serious and ongoing condition like poor nutrition. Fish like tangs that are especially vulnerable to this condition should be fed a varied diet high in fresh macroalgae. Vitamin supplements can also be helpful. Some research suggests that HLLE can also be caused at least in part by other stresses like some flagellate parasites or stray electrical current.

Hole-in-the-head Disease (  E ,  P ): Hole-in-the-head is very similar to HLLE, described above. Some aquarists argue that these two names refer to the freshwater and saltwater versions of the same condition since they share some of the same causes and symptoms. Hole-in-the-head is found mostly with large cichlids like Oscars and Discus but can affect other fish as well. Like HLLE, the main cause is usually linked to improper diet or water conditions and adding vitamin supplements and a varied diet can often help stop and reverse some of the effects of the disease. Hole-in-the-head is also attributed more to parasite infections than HLLE, specifically protozoans.

“Ich” ( P ): Ichthyophthirius multifiliis, also known as Ich, Ick, or White Spot, is one of the most common and well-known conditions in the aquarium hobby. Many aquarists incorrectly diagnose problems with their aquarium as ich when it is actually another condition. Ich is a parasite that affects freshwater fish (as opposed to the similar Cryptocaryon that affects saltwater fish but has an almost identical appearance, symptoms and treatment). Ich appears as small white spots on the body of the fish. These spots look like grains of salt as opposed to the cottony tufts of fungal infections, the dust-like appearance of oodinium or some bacterial infections or the pits associated with Hole-in-the-head and HLLE. The fish may stop eating, may scratch and rub against surfaces, and may appear lethargic. Treatments include increasing temperature, adding vitamin and garlic supplements, freshwater or saltwater “dips”, and a score of medications. The parasite also has a life cycle that allows it to remain dormant in an aquarium or on a fish for weeks at a time before blooming when triggered by environmental conditions or the fish’s immune system being weakened by stress or anther condition. Some medications available to treat ich are not safe for all fish or for invertebrates; be sure to choose the medication suitable for your aquarium. 

Internal Parasites ( P ): Internal parasites can be diagnosed externally by white, stringy feces and a sunken stomach or eyes as the parasite steals the nutrients from the fish. Internal parasite - most commonly types of worms - can affect the fish most commonly from infected live or fresh foods. External medications that are added to the water are less effective on internal parasites. It is best to treat the fish's food by soaking the food in a medicated solution before feeding. Garlic supplements and other vitamins also may help expel the parasite and help the fish replenish its nutrients and fight off the parasite on its own. 

“Lymph” (Virus): Lymphocystis, commonly known as “lymph”, is a virus that affects both freshwater and saltwater fish. This virus forms white cauliflower-like growths on the fins and body of the fish and can cause white patches around the eyes. It usually develops when the immune system of the fish is weakened due to poor nutrition or water quality. Being a virus, there is no reliable medication to treat it but improving the conditions and diet will help to boost the fish’s natural immune system and can help the fish fight it on their own. Some sources recommend removing the nodules by scraping them from the body or fins; this can be a dangerous approach that may lead to excessive stress and secondary infections. Lymph is not usually fatal and often may clear up on its own as the fish fights off the virus.

Marine Velvet/ Oodinium ( P ): Marine Velvet, also known as Oodinium, is caused by the parasite Amyloodinium ocellatum. This is one of the most fatal parasitic infections as it is very contagious and resistant to most medications. Marine Velvet looks like a very fine velvety coating on the fish as opposed to the salt-like spotting of Ich. The fish may also breathe rapidly and have cloudy eyes. Quarantine and treat any affected fish as soon as possible with a strong antiparasitic treatment like copper sulfates. The salinity can also be lowered and a UV sterilizer can be used to help kill the parasites.

"Neon Tetra Diseases" (NTD) ( P ):  Despite the common name, this condition affects many more species than just Neon Tetras; most freshwater fish like tetras, danios, rasboras, rainbowfish and more can be affected. It typically first appears like a saddle extending around the dorsal fin on the back of the fish similar to the Columnaris infection described above. Rather than the fuzzy, wispier look to Columnaris patches, NTD looks more like the color and scales have been “erased” from the area. The fish may swim erratically or its body may start to appear bend downward at the spine.  NTD is caused by a Microsporidian parasite. This is an internal parasite that starts affecting the fish from the inside rather than the external parasites like Ich more commonly encountered. This parasite can be highly contagious and is usually spread by eating infested foods or fish flesh. There is no effective treatment for this condition. Once a fish shows symptoms, it is best to move it into a separate quarantine system or euthanize it to avoid spreading the parasite to other fish. 

Pop-eye( B ,  E ): Like the name suggests, “pop-eye” is a condition in which one or both eyes of the fish appear to be swollen and popping out of the socket. This can result from a bacterial infection, poor water quality, injury or in rare cases a gas pocket in the eye socket. This is typically a symptom of an underlying condition like poor water quality and is difficult to treat specifically. Anti-bacterial medications may help but the water quality and any other possible causes should be addresses as well. Pop-eye may often clear on its own but may lead to decreased vision in the affected eye.

Scar Tissue/Cysts( E ):  Sometimes confused with Ich, these irregular lumps are usually only along the spines in the fins. They are caused by a blood vessel blockage or scar tissue due to broken spines, poor breeding, poor water quality, or stress. It can sometimes - but not usually - be an early sign of or lead to a secondary disease like Fin Rot. They are usually seen in fish with larger fins like Angelfish, Guppies, Bettas or selectively-bred longfin varieties of other fish. Usually benign and harmless, they are not usually treatable but usually disappear on their own.

Septicemia( B ,  E ): Septicemia is an infection in the blood. The infection itself is bacterial but usually occurs when a fish is left vulnerable due to poor water conditions. It appears as red streaks in the fins and body and open sores or deteriorating fins in more severe cases. Any environmental conditions like poor water quality must be improved and resolved as quickly as possible. External bacterial medications in the water may help but pretreating the food with medication and using internal bacterial medications is more effective. Catching this infection as soon as possible drastically improves survival rates.

Swim Bladder Infection/Disorders ( E ): This condition is seen mostly in fancy goldfish, balloon mollies and other fish bred for a similar “chubby” body shape. The swim bladder in fish is used to help control buoyancy (the up and down motion) through gas exchange within the fish’s body. The fish is considered “neutrally buoyant” when it is able to hover in the water without floating up or sinking down. If the fish is unable to achieve buoyancy, it may float, sink or be unable to swim properly or remain upright in the water. This may be the result of an internal bacterial infection that can be treated with some medications. Some fish, especially fancy goldfish, may gulp air at the surface will feeding and have similar issues caused by air in their digestive systems. Feeding them fresh greens like peas or zucchini may help get rid of this bubble.

Overhere a PDF file with a resumé of fish diseases which you may download.